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An integrated software system for analyzing ChIP-chip and ChIP-seq data - Nature Biotechnology

  • ️Wong, Wing H
  • ️Sun Nov 02 2008
  • Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499–509 (2004).

    Article  CAS  Google Scholar 

  • Boyer, L.A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).

    Article  CAS  Google Scholar 

  • Carroll, J.S. et al. Genome-wide analysis of estrogen receptor binding sites. Nat. Genet. 38, 1289–1297 (2006).

    Article  CAS  Google Scholar 

  • Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007).

    Article  CAS  Google Scholar 

  • Robertson, G. et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651–657 (2007).

    Article  CAS  Google Scholar 

  • Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).

    Article  CAS  Google Scholar 

  • Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

    Article  CAS  Google Scholar 

  • Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106–1117 (2008).

    Article  CAS  Google Scholar 

  • Wederell, E.D. et al. Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res. 36, 4549–4564 (2008).

    Article  CAS  Google Scholar 

  • Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521–533 (2008).

    Article  CAS  Google Scholar 

  • Johnson, W.E. et al. Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl. Acad. Sci. USA 103, 12457–12462 (2006).

    Article  CAS  Google Scholar 

  • Ji, H. & Wong, W.H. TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 21, 3629–3636 (2005).

    Article  CAS  Google Scholar 

  • Kampa, D. et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331–342 (2004).

    Article  CAS  Google Scholar 

  • Zheng, M., Barrera, L.O., Ren, B. & Wu, Y.N. ChIP-chip: data, model, and analysis. Biometrics 63, 787–796 (2007).

    Article  CAS  Google Scholar 

  • Keles, S. Mixture modeling for genome-wide localization of transcription factors. Biometrics 63, 10–21 (2007).

    Article  CAS  Google Scholar 

  • Ghosh, S., Hirsch, H.A., Sekinger, E., Struhl, K. & Gingeras, T.R. Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. BMC Bioinformatics 7, 434 (2006).

    Article  Google Scholar 

  • Du, J. et al. A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics 22, 3016–3024 (2006).

    Article  CAS  Google Scholar 

  • Qi, Y. et al. High-resolution computational models of genome binding events. Nat. Biotechnol. 24, 963–970 (2006).

    Article  CAS  Google Scholar 

  • Scacheri, P.C., Crawford, G.E. & Davis, S. Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol. 411, 270–282 (2006).

    Article  CAS  Google Scholar 

  • Bieda, M., Xu, X., Singer, M.A., Green, R. & Farnham, P.J. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 16, 595–605 (2006).

    Article  CAS  Google Scholar 

  • Zhang, Z.D. et al. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol. 8, R81 (2007).

    Article  Google Scholar 

  • Song, J.S. et al. Model-based analysis of two-color arrays (MA2C). Genome Biol. 8, R178 (2007).

    Article  Google Scholar 

  • Reiss, D.J., Facciotti, M.T. & Baliga, N.S. Model-based deconvolution of genome-wide DNA binding. Bioinformatics 24, 396–403 (2008).

    Article  CAS  Google Scholar 

  • Song, J.S. et al. Microarray blob-defect removal improves array analysis. Bioinformatics 23, 966–971 (2007).

    Article  CAS  Google Scholar 

  • Liu, X.S., Brutlag, D.L. & Liu, J.S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835–839 (2002).

    Article  CAS  Google Scholar 

  • Hong, P. et al. A boosting approach for motif modeling using ChIP-chip data. Bioinformatics 21, 2636–2643 (2005).

    Article  CAS  Google Scholar 

  • Shim, H. & Keles, S. Integrating quantitative information from ChIP-chip experiments into motif finding. Biostatistics 9, 51–65 (2008).

    Article  Google Scholar 

  • Ji, X., Li, W., Song, J., Wei, L. & Liu, X.S. CEAS: cis-regulatory element annotation system. Nucleic Acids Res. 34, W551–554 (2006).

    Article  CAS  Google Scholar 

  • Albert, I., Wachi, S., Jiang, C. & Pugh, B.F. GeneTrack–a genomic data processing and visualization framework. Bioinformatics 24, 1305–1306 (2008).

    Article  CAS  Google Scholar 

  • Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5, 829–834 (2008).

    Article  CAS  Google Scholar 

  • Jothi, R., Cuddapah, S., Barski, A., Cui, K. & Zhao, K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 36, 5221–5231 (2008).

    Article  CAS  Google Scholar 

  • Wheeler, D.L. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 36, D13–D21 (2008).

    Article  CAS  Google Scholar 

  • Karolchik, D. et al. The UCSC genome browser database: 2008 update. Nucleic Acids Res. 36, D773–D779 (2008).

    Article  CAS  Google Scholar 

  • Flicek, P. et al. Ensembl 2008. Nucleic Acids Res. 36, D707–D714 (2008).

    Article  CAS  Google Scholar 

  • Liu, J.S., Neuwald, A.F. & Lawrence, C.E. Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J. Am. Stat. Assoc. 90, 1156–1170 (1995).

    Article  Google Scholar 

  • Zhou, Q. & Wong, W.H. CisModule: de novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl. Acad. Sci. USA 101, 12114–12119 (2004).

    Article  CAS  Google Scholar 

  • Ji, H., Vokes, S.A. & Wong, W.H. A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors. Nucleic Acids Res. 34, e146 (2006).

    Article  Google Scholar 

  • Chen, Z.F., Paquette, A.J. & Anderson, D.J. NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis. Nat. Genet. 20, 136–142 (1998).

    Article  CAS  Google Scholar 

  • Chong, J.A. et al. REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons. Cell 80, 949–957 (1995).

    Article  CAS  Google Scholar 

  • Matys, V. et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34, D108–D110 (2006).

    Article  CAS  Google Scholar 

  • Johnson, D.S. et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 18, 393–403 (2008).

    Article  Google Scholar 

  • Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 28–36. AAAI Press, Menlo Park, California, USA, (1994).

  • Giardine, B. et al. Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005).

    Article  CAS  Google Scholar 

  • Crooks, G.E., Hon, G., Chandonia, J.M. & Brenner, S.E. WebLogo: A sequence logo generator. Genome Res. 14, 1188–1190 (2004).

    Article  CAS  Google Scholar 

  • The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).

  • Euskirchen, G.M. et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 17, 898–909 (2007).

    Article  CAS  Google Scholar 

  • Jiang, H. & Wong, W.H. SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24, 2395–2396 (2008).

    Article  CAS  Google Scholar 

  • Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).

    Article  CAS  Google Scholar 

  • Schmid, C.D. & Bucher, P. ChIP-Seq data reveal nucleosome architecture of human promoters. Cell 131, 831–832 (2007).

    Article  CAS  Google Scholar